Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,312,730	0	A	T	77.8%	64.7 / 21.4	36	S88T (TCT→ACT)	alsR	DNA‑binding transcriptional repressor AlsR
Reads supporting (aligned to +/- strand):  ref base A (6/2);  new base T (11/17);  total (17/19)
Fisher's exact test for biased strand distribution p-value = 1.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.11e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGTCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGAAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCTTCAGATACCGCCAGAGCTTCTGCGACATCTTTAATTGCGGGTGCACAACTCAGGTTACCGGGTTTGAGTAACCACTCCACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTTCATTCGCAGGTAAGGCGCTAACCCTATACCGTTCGGAAGCGCTGAAT  >  NC_000913/4312493‑4312972                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                   cAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGTCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTcc                                                                                                                                                                                                                                       >  2:294484/1‑251 (MQ=255)              cTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGTCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGt                                                                                                                                                                                                                           >  1:194465/1‑250 (MQ=255)                   gCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGTCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTGGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTAAGTTa                                                                                                                                                                                                                     <  2:39113/251‑1 (MQ=255)                        aCATCAGCTCAGATAGCATTTGATCCTCCGGCACCGGTCTAATCCCGCTGTCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGGTGACTATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCTGAAGGCAATACCTGTTCTGACTGAGTAAAATATTCTTCCAGCGCACTGCGTAAGTTACGaaa                                                                                                                                                                                                                <  2:187768/251‑1 (MQ=255)                          aTCAGCACAGATAGCATGTGATCCTCCGGCACCGGACAAATCCCGCGGTCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACTTTGACGATCGACTGACCTGCCATAATGGTGCTTAAAGTGATGTTAAATACCTTAGGCACCACATCCGGCGGCGCTGCATCTAAAGCCATCTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTGCCAGCGCACTTCGTAAgatagaaaagc                                                                                                                                                                                                              <  2:336789/251‑11 (MQ=255)                           tCAGCACAGATAGCATTTGATCCTCCGGAACCGAACACATCCCGCTGTCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATATCATAAACGTTGACGATCGTCTGACATTCCATAATGGAGCGTAAAGTGATGATAAATACCTTATTCACCACATACTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGAGTAAGTTACGAAAgac                                                                                                                                                                                                             >  1:389701/1‑249 (MQ=255)                                   gATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGTCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAAcc                                                                                                                                                                                                     >  1:32753/1‑251 (MQ=255)                                    aTAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGTCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGAAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAAccc                                                                                                                                                                                                    >  1:141533/1‑251 (MQ=255)                                           ttGATCCTCCGGCACCGTACAAATCCCGCTGTCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTa                                                                                                                                                                                                                          >  1:237882/1‑222 (MQ=255)                                           ttGATCCTCCGGCACCGTACAAATCCCGCTGTCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTa                                                                                                                                                                                                                          <  2:237882/222‑1 (MQ=255)                                                   ccGGCACCGTACAAATCCCGCTGTCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGAAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATAc                                                                                                                                                                                     >  1:41357/1‑251 (MQ=255)                                                          cGTACAAATCCCGCTGTCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACt                                                                                                                                                                              <  1:320155/251‑1 (MQ=255)                                                                    ccGCTGTCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGAAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCtt                                                                                                                                                                    <  2:41357/251‑1 (MQ=255)                                                                             ggCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCTTCAGATACCg                                                                                                                                                           <  1:73033/251‑1 (MQ=255)                                                                                                 cggcACGGTGGATCTAATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCTTCAGATACCGCCAGAGCTTCTGCGACATCt                                                                                                                                       >  1:310739/1‑251 (MQ=255)                                                                                                     actgTGGATCTCATCAACGTTGACGTTCGACTGACCGTCCATAATGGTGCGTAAAGTGATGTTAAATCCCTTATTCACCACAGCCGGCGTCGCTTCATCAAAAGCCATCTCGGAAGGCAATCCCTGTTCTGACGGAGTAAAATAATCTTCCAGCGCACTGCGTAAGTTACGaaa                                                                                                                                                                                                                <  2:232715/171‑1 (MQ=255)                                                                                                     aCGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTAAGTTACGaaa                                                                                                                                                                                                                >  1:232715/1‑174 (MQ=255)                                                                                                                     aCGTTGACGATCGTATGACCTGCCAGAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGAGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCTTCAGATACCGCCAGAGCTTCTGCGACATCGTTAATTGCGGGTGCACAACt                                                                                                                   <  2:316199/251‑1 (MQ=255)                                                                                                                      cGTTGACGATCGACTGACCTTCCATAATGGCGCGAAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGAAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCTTCAGATACCGCCAGAGCTTCTGCGACATCTTTAATTGCGGGTGCACAACTc                                                                                                                  >  1:368691/1‑251 (MQ=255)                                                                                                                       gTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCTTCAGATACCGCCAGAGCTTCTGCGACATCTTTAATTGCGGGTGCACAACTCa                                                                                                                 <  1:294484/251‑1 (MQ=255)                                                                                                                             gATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGAAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCTTCAGATACCGCCAGAGCTTCTGCGACATCTTTAATTGCGGGTGCACAACTCAGGTTAc                                                                                                           >  1:52613/1‑251 (MQ=255)                                                                                                                              aTCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCTTCAGATACCGCCAGAGCTTCTGCGACATCTTTAATTGCGGGTGCACAACTCAGGTTAcc                                                                                                          >  1:289302/1‑251 (MQ=255)                                                                                                                                 gACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGAAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCTTCGCTTCAGATACCGCCAGAGCTTCTGCGACATCTTTAATTGCTGGTGCACAACTCAGGTTACCggg                                                                                                       >  2:98815/1‑251 (MQ=255)                                                                                                                                              tAATGGTGCGTAAAGTGATGTTAAATACCTTCTTCACAACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACATGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAg                                                                                                                                                                                                               >  1:384648/1‑134 (MQ=255)                                                                                                                                              tAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAg                                                                                                                                                                                                               <  2:384648/134‑1 (MQ=255)                                                                                                                                                           aGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGATTGAGAAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCTTCAGATACCGCCAGAGCTTCTGCGACATCTTTAATTGCGGGTGCACAACTCAGGTTACCGGGTTTGAGTAACCACTCCACGATGCGGc                                                                             >  1:161091/1‑251 (MQ=255)                                                                                                                                                                    aaaTACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCTCTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCTTCAGATACCGCCAGAGCTTCTGCGACATCTTTAATTGCGGGTGCACAACTCAGGTTACCGGGTTTGAGTAACCACTCCACGATGCGGCTTTCAtttt                                                                    <  2:194465/251‑1 (MQ=255)                                                                                                                                                                                caccacATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCACTACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGCTACCTTAACTATCATCGCTTCAGATACCGCCAGAGCTTCTGCGACATTTTTAATTGCGGGTGCACAACTCAGGTTACCGGGTTTGAGTAACCACTCCACGCTGCGGCTTTCATTTTCTGTCAttcctt                                                        >  1:35056/1‑251 (MQ=255)                                                                                                                                                                                     caTCCTGCGGCGCGTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCTTCAGATACCGCCAGAGCTTCTGCGACATCTTTAATTGCGGGTGCACAACTCAGGTTACCGGGTTTGAGTAACCACTCCACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGc                                                   <  2:289302/251‑1 (MQ=255)                                                                                                                                                                                                     atcaAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGAAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCTTCAGATACCGCCAGAGCTTCTGCGACATCTTTAATTGCGGGTGCACAACTCAGGTTACCGGGTTTGAGTAACCACTCCACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTTCATTCGCAGGTAAg                                   <  1:302383/251‑1 (MQ=255)                                                                                                                                                                                                       caAAAGCCAACGCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCTTCAGATACCGCCAGATCTTCTGCGACAGCGTTAAGTGCGGTTGCCCAACGCAGGTTACCGGGGTTGAGTGACCACTCCACGATGCGGTGTTCATTTTCTGTCATTACGTCCTGCTTCATTCGCAGTTAAgg                                  <  2:376431/250‑1 (MQ=255)                                                                                                                                                                                                              cAACTCGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCTTCAGATACCGCCAGAGCTTCTGCGACATCTTTAATTGCGGGTGCACAACTCAGGTTACCGGGTTTGAGTAACCACTCCACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTTCATTCGCAGGTAAGGCGCTAAcc                          >  1:409809/1‑251 (MQ=255)                                                                                                                                                                                                                   cGGAAGGCAATACCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATTCCTTAACTATCATCGCTTCAGATACCGCCAGAGCTTCTGCGACATCTGTAATTGCGGGTGCACAACTCAGGTTACCGGGTTTGAGTAACCACTCCGCGATGCGGCTTTCATTTTCTGTCATTCCGGCCTGCTGCAGTCGCAGGTAAGGCGCTAACCCtata                     <  2:409809/251‑1 (MQ=255)                                                                                                                                                                                                                              aCCTGTTCTGACTGAGTAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCTTCAGATACCGCCAGAGCTTCTGCGACATCTTTAATTGCGGGTGCACAACTCAGGTTACCGGGTTTGAGTAACCACTCCACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTTCATTCGCAGGTAAGGCGCTAACCCTATACCGTTCGGaa           <  1:386799/250‑1 (MQ=255)                                                                                                                                                                                                                                       gactgaGTAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCTTCAGATACCGCCAGAGCTTCTGCGACATCTTTAATTGCGGGTGCACAACTCAGGTTACCGGGTTTGAGTAACCACTCCACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTTCATTCGCAGGTAAGGCGCTAACCCTATACCGTTCGGAAGCGCTGAAt  <  1:215041/250‑1 (MQ=255)                                                                                                                                                                                                                                       gactgaGTAAAATAATCGTCCAGCGCACTGCGTAAGTGACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCTTCAGATACCGCCAGAGCTTCTGCGACATCTTTAATTGCGGGTGCACAACTCAGGTTACCGGGTTTGAGTAACCACTCCACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTTCATTCGCAGGTAAGGCGCTAACCCTATACCGTTCGGAAGCGCTGAAt  <  1:419612/250‑1 (MQ=255)                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                   CAATGCGCAAGAACTTGTGCTGTACATCAGCACAGATAGCATTTGATCCTCCGGCACCGTACAAATCCCGCTGTCTGGCCTGATAGAAAAAGCGGGCGGCACGGTGGATCTCATCAACGTTGACGATCGACTGACCTTCCATAATGGTGCGTAAAGTGATGTTAAATACCTTATTCACCACATCCTGCGGCGCTTCATCAAAAGCCAACTCGGAAGGCAATACCTGTTCTGACTGAGAAAAATAATCTTCCAGCGCACTGCGTAAGTTACGAAAGCCGCTAAACCCCAGCAGCTTTGATACCTTAACTATCATCGCTTCAGATACCGCCAGAGCTTCTGCGACATCTTTAATTGCGGGTGCACAACTCAGGTTACCGGGTTTGAGTAACCACTCCACGATGCGGCTTTCATTTTCTGTCATTCCTTCCTGCTTCATTCGCAGGTAAGGCGCTAACCCTATACCGTTCGGAAGCGCTGAAT  >  NC_000913/4312493‑4312972

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑